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Tue, 26 Sep 2017 12:18:22 +0000en-UShourly1http://wordpress.org/?v=4.2.16Ed in the microarray have previously been annotated as imprinted genes.http://www.pi4kinhibitor.com/2017/09/26/ed-in-the-microarray-have-previously-been-annotated-as-imprinted-genes/
http://www.pi4kinhibitor.com/2017/09/26/ed-in-the-microarray-have-previously-been-annotated-as-imprinted-genes/#commentsTue, 26 Sep 2017 12:18:22 +0000http://www.pi4kinhibitor.com/?p=4193Ed in the microarray have previously been annotated as imprinted genes. GRB10 and ATP10A were upGDC-0810 chemical information regulated in parthenotes, as expected because the maternal allele is the one expressed, while ZNF215, NDN, IMPACT and SFMBT2 were downregulated according to the paternal allele expression. Furthermore, 26 other genes of the microarray which were significantly different in parthenote embryos, also shown to have at least one member of that gene family imprinted in other species (Table 6).DiscussionOur results demonstrated that parthenotes and in vivo fertilised rabbit blastocysts cultured under in vivo conditions differ notably in gene expression. Up till now, few works have analysed transcriptome differences between parthenotes and fertilised embryosTranscriptome of In Vivo Parthenote BlastocystsTable 6. Putative imprinted genes differentially expressed in parthenogenetic late blastocysts identified as family members at Catalogue of Imprinted Genes (http://igc.otago.ac.nz/home.html).Family members genes name Imprinted gene SLC22A2, SLC22A3, SLC22A8, SLC22A18S AWT1,WT1-AS IGF2 RB1 L3MBTL PPP1RGA ASB4 KLF14 NAP1L5 UPS29 ZFP264, ZFP127 PEC2, PEC3 NCCR UBE3A TSPAN32 TNFRSF23 ANO1 INPP5F-V2 RASGRF1 COMMD1 HTR2A FBXO40 SNRPN PRIM2 CDKN1C SASH2 doi:10.1371/journal.pone.0051271.t006 CDKN1A, CDKN1B, CDKN3 SASH1 FBXO15, FBXO32, FBXO48 INPP1, INPP4B RASGEF1B, RASGRP3 COMMD3, COMMD5 RASGRP1, RASGRP2 COMMD2, COMMD7, COMMD8 HTRA4 FBXO4, FBXO5, FBXO25, FBXO38, FBXO42 SNRPPA1, SNRPB2 PRIM1 UBE3B, UBE4B TSPAN5, TSPAN12, TSPAN13 TSPAN1N, TSPAN14, TSPAN31 TNFRSF1A ANO6 ASB8 KLF16, KLF12 NAP1L1 USP2, USP4, USP25, USP53 USP7, USP15, USP22, USP28, USP34USP40, USP43, USP46, USP48 ZFP36, ZFP57, ZFP62, ZFP90 PECR NCCRP1 IGF2BP2 RB11A L3MBTL2 L3MBTL1 PPP1CC ASB3 KLF3, KLF4 Upregulated Downregulated SLC22A5, SLC22A17 SWT1 IGF2BP[20,21,22]. However, these works were carried out with parthenote embryos developed in vitro and in vitro cultured fertilised embryos. It is well documented that embryos developed under in vitro environment are still not comparable with in vivo embryos [23], as post-fertilisation culture environment is a determinant for adequate embryonic development [4,24]. For example, one of the most critical time points of preimplantation embryogenesis is the major embryonic genome activation 1317923 at which the embryo switches from using the mRNA and proteins derived from the maternal genome to those resulting from de novo transcription from the embryonic genome [25]. During that time, availability of transcription factors, which are regulated by cell cycle-dependent mechanisms, is required [26]. These mechanisms are strongly influenced by a change in environmental conditions and subsequently affect the embryonic development, with potentially severe effects on foetal, prenatal and postnatal viability [27]. Corcoran et al. [20] found that a total of 384 genes were differentially expressed between in vivo and in vitro derived blastocysts, the vast majority of them (almost 85 ) being downregulated in in vitro developed embryos. Likewise, the effects of developmental environment on mRNA purchase Ganetespib expression in parthenogenetic embryos have also been described [11] this way. To our best knowledge, this is the first report that compared the genome-wide gene expression profiles between rabbit parthenogenetic blastocysts and fertilised blastocysts developed in vivo. Microarray analysis of parthenotes and fertilised embryos developed in vitro indicated differences in expression of 749.Ed in the microarray have previously been annotated as imprinted genes. GRB10 and ATP10A were upregulated in parthenotes, as expected because the maternal allele is the one expressed, while ZNF215, NDN, IMPACT and SFMBT2 were downregulated according to the paternal allele expression. Furthermore, 26 other genes of the microarray which were significantly different in parthenote embryos, also shown to have at least one member of that gene family imprinted in other species (Table 6).DiscussionOur results demonstrated that parthenotes and in vivo fertilised rabbit blastocysts cultured under in vivo conditions differ notably in gene expression. Up till now, few works have analysed transcriptome differences between parthenotes and fertilised embryosTranscriptome of In Vivo Parthenote BlastocystsTable 6. Putative imprinted genes differentially expressed in parthenogenetic late blastocysts identified as family members at Catalogue of Imprinted Genes (http://igc.otago.ac.nz/home.html).Family members genes name Imprinted gene SLC22A2, SLC22A3, SLC22A8, SLC22A18S AWT1,WT1-AS IGF2 RB1 L3MBTL PPP1RGA ASB4 KLF14 NAP1L5 UPS29 ZFP264, ZFP127 PEC2, PEC3 NCCR UBE3A TSPAN32 TNFRSF23 ANO1 INPP5F-V2 RASGRF1 COMMD1 HTR2A FBXO40 SNRPN PRIM2 CDKN1C SASH2 doi:10.1371/journal.pone.0051271.t006 CDKN1A, CDKN1B, CDKN3 SASH1 FBXO15, FBXO32, FBXO48 INPP1, INPP4B RASGEF1B, RASGRP3 COMMD3, COMMD5 RASGRP1, RASGRP2 COMMD2, COMMD7, COMMD8 HTRA4 FBXO4, FBXO5, FBXO25, FBXO38, FBXO42 SNRPPA1, SNRPB2 PRIM1 UBE3B, UBE4B TSPAN5, TSPAN12, TSPAN13 TSPAN1N, TSPAN14, TSPAN31 TNFRSF1A ANO6 ASB8 KLF16, KLF12 NAP1L1 USP2, USP4, USP25, USP53 USP7, USP15, USP22, USP28, USP34USP40, USP43, USP46, USP48 ZFP36, ZFP57, ZFP62, ZFP90 PECR NCCRP1 IGF2BP2 RB11A L3MBTL2 L3MBTL1 PPP1CC ASB3 KLF3, KLF4 Upregulated Downregulated SLC22A5, SLC22A17 SWT1 IGF2BP[20,21,22]. However, these works were carried out with parthenote embryos developed in vitro and in vitro cultured fertilised embryos. It is well documented that embryos developed under in vitro environment are still not comparable with in vivo embryos [23], as post-fertilisation culture environment is a determinant for adequate embryonic development [4,24]. For example, one of the most critical time points of preimplantation embryogenesis is the major embryonic genome activation 1317923 at which the embryo switches from using the mRNA and proteins derived from the maternal genome to those resulting from de novo transcription from the embryonic genome [25]. During that time, availability of transcription factors, which are regulated by cell cycle-dependent mechanisms, is required [26]. These mechanisms are strongly influenced by a change in environmental conditions and subsequently affect the embryonic development, with potentially severe effects on foetal, prenatal and postnatal viability [27]. Corcoran et al. [20] found that a total of 384 genes were differentially expressed between in vivo and in vitro derived blastocysts, the vast majority of them (almost 85 ) being downregulated in in vitro developed embryos. Likewise, the effects of developmental environment on mRNA expression in parthenogenetic embryos have also been described [11] this way. To our best knowledge, this is the first report that compared the genome-wide gene expression profiles between rabbit parthenogenetic blastocysts and fertilised blastocysts developed in vivo. Microarray analysis of parthenotes and fertilised embryos developed in vitro indicated differences in expression of 749.
]]>http://www.pi4kinhibitor.com/2017/09/26/ed-in-the-microarray-have-previously-been-annotated-as-imprinted-genes/feed/0Ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi??(TPzFP)|(TPzFN)|(TNzFP)|(TNzFN) Where TP is the number ofhttp://www.pi4kinhibitor.com/2017/09/26/ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffitpzfptpzfntnzfptnzfn-where-tp-is-the-number-of/
http://www.pi4kinhibitor.com/2017/09/26/ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffitpzfptpzfntnzfptnzfn-where-tp-is-the-number-of/#commentsTue, 26 Sep 2017 08:17:17 +0000http://www.pi4kinhibitor.com/?p=4191Ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi??(TPzFP)|(TPzFN)|(TNzFP)|(TNzFN) Where TP is the number of true positives; FN, the false negatives; TN, the true negatives; FP, the false positives, PPV, the probability of positive prediction; and MCC, Matthews Correlation Coefficient. Additionally, the sensitivity of each SVM model was tested separately against each peptide class: a-defensins, b-defensins, CSab defensins, cyclotides, hepcidins, hevein-like peptides, knottins, panaedins, tachplesins, h-defensins, thionins and undefined. The group of undefined peptides encompasses peptides without a defined class and classes with fewer than five members. Furthermore, the 1364 sequences from PDB that were not included in NS were used for verifying the specificity of models.membrane proteins [20]. There is an order Fexaramine overlapping between the positive BS1 and BS2 sequences, once they were extracted from APD. Nevertheless there is no overlapping between the negative sequences, once in BS1 they were extracted from PDB. Furthermore the sequences from BS2 were randomly generated clearly showing any coinciding. A third assessment was done with the weighted average of the two benchmarks. BS1 and BS2 are available as Data Sets S1 and S2, respectively, in fasta format.Results and DiscussionThe cysteine patterns are widely spread in several classes of biologically active peptides. These patterns are highly conserved and are responsible for keeping stable the structural folding. For this reason they are used for peptide classification [4,20,27]. Due to their multifunctionality, they have an enormous biotechnology potential [1,2,31,32]. However, due to their multifunctional character, the identification of a single function without in vitro and/or in vivo tests is a very difficult task. As an example, we can cite the cyclotide parigidin-br1. This peptide was identified in leaves of Palicurea rigida [8] but was unable to control bacterial development, despite sharing 75 of identity with a bactericidal cyclotide named circulin b [42]. Among the possible activities, the TER199 antimicrobial one is a good target for prediction, since there are several databases dedicated to peptides with this kind of activity, 1317923 such as APD [35] and CAMP [23]. Several models of antimicrobial activity prediction have been proposed by using such databases [20?5]. On the other hand, there are no non-antimicrobial peptide databases, which becomes an enormous challenge for constructing reliable models [20,21,25]. Several approaches have been proposed to overcome this problem, including the use of proteins with the annotation of non-antimicrobial from SwissProt or PDB [21,23?5] or even using sequences predicted to have signal peptides or trans-BenchmarkingThe blind data set was used to compare the models generated in this study with the algorithms SVM, Discriminant Analysis (DA), and Random Forest (RF) from the Collection of Antimicrobial Peptides (CAMP) [23], an artificial neuro fuzzy inference system (ANFIS) [25] and also the SVM model generated by our previous work [20]. The assessment of each model was done through the parameters described in equations 1 to 5. Additionally, the blind data set from our previous work (BS2) [20] was also used as a second benchmarking assessment. BS2 is composed of 53 antimicrobial sequences with six cysteine residues extracted from APD and 53 proteins randomly generated.Ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi??(TPzFP)|(TPzFN)|(TNzFP)|(TNzFN) Where TP is the number of true positives; FN, the false negatives; TN, the true negatives; FP, the false positives, PPV, the probability of positive prediction; and MCC, Matthews Correlation Coefficient. Additionally, the sensitivity of each SVM model was tested separately against each peptide class: a-defensins, b-defensins, CSab defensins, cyclotides, hepcidins, hevein-like peptides, knottins, panaedins, tachplesins, h-defensins, thionins and undefined. The group of undefined peptides encompasses peptides without a defined class and classes with fewer than five members. Furthermore, the 1364 sequences from PDB that were not included in NS were used for verifying the specificity of models.membrane proteins [20]. There is an overlapping between the positive BS1 and BS2 sequences, once they were extracted from APD. Nevertheless there is no overlapping between the negative sequences, once in BS1 they were extracted from PDB. Furthermore the sequences from BS2 were randomly generated clearly showing any coinciding. A third assessment was done with the weighted average of the two benchmarks. BS1 and BS2 are available as Data Sets S1 and S2, respectively, in fasta format.Results and DiscussionThe cysteine patterns are widely spread in several classes of biologically active peptides. These patterns are highly conserved and are responsible for keeping stable the structural folding. For this reason they are used for peptide classification [4,20,27]. Due to their multifunctionality, they have an enormous biotechnology potential [1,2,31,32]. However, due to their multifunctional character, the identification of a single function without in vitro and/or in vivo tests is a very difficult task. As an example, we can cite the cyclotide parigidin-br1. This peptide was identified in leaves of Palicurea rigida [8] but was unable to control bacterial development, despite sharing 75 of identity with a bactericidal cyclotide named circulin b [42]. Among the possible activities, the antimicrobial one is a good target for prediction, since there are several databases dedicated to peptides with this kind of activity, 1317923 such as APD [35] and CAMP [23]. Several models of antimicrobial activity prediction have been proposed by using such databases [20?5]. On the other hand, there are no non-antimicrobial peptide databases, which becomes an enormous challenge for constructing reliable models [20,21,25]. Several approaches have been proposed to overcome this problem, including the use of proteins with the annotation of non-antimicrobial from SwissProt or PDB [21,23?5] or even using sequences predicted to have signal peptides or trans-BenchmarkingThe blind data set was used to compare the models generated in this study with the algorithms SVM, Discriminant Analysis (DA), and Random Forest (RF) from the Collection of Antimicrobial Peptides (CAMP) [23], an artificial neuro fuzzy inference system (ANFIS) [25] and also the SVM model generated by our previous work [20]. The assessment of each model was done through the parameters described in equations 1 to 5. Additionally, the blind data set from our previous work (BS2) [20] was also used as a second benchmarking assessment. BS2 is composed of 53 antimicrobial sequences with six cysteine residues extracted from APD and 53 proteins randomly generated.
]]>http://www.pi4kinhibitor.com/2017/09/26/ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffitpzfptpzfntnzfptnzfn-where-tp-is-the-number-of/feed/0H trial were randomized, but never included the goal arm, whichhttp://www.pi4kinhibitor.com/2017/09/26/h-trial-were-randomized-but-never-included-the-goal-arm-which/
http://www.pi4kinhibitor.com/2017/09/26/h-trial-were-randomized-but-never-included-the-goal-arm-which/#commentsTue, 26 Sep 2017 05:49:19 +0000http://www.pi4kinhibitor.com/?p=4189H trial were randomized, but never included the goal arm, which remained the same throughout all trials. If the rat could not find the platform within 1 minute, it was guided to and allowed to sit on the platform during the intertrial interval. During the 1-minute intertrial interval, BU-4061T cost animals remained on the platform. The 12 acquisition trials were divided into two blocks of six consecutive trials, interspersed with a 5-minute break. Following the acquisition trials, the animals underwent a short-term memory trial (30 minutes later) and a long-term memory trial (24 hours later). For each trial, latency to locate the platform and number of errors were recorded. Errors were operationally defined as anytime the animal’s entire body entered an arm that was not the goal arm, as well as anytime an animal entered the goal arm but did not find the hidden platform.Corticosterone AssessmentTo verify that CUS and learning experience were stressful, we assessed corticosterone levels, using fecal boli, since they can be obtained without stress to the animal and fecal corticosterone is highly correlated with serum corticosterone [22,23]. Fecal boli were collected from 12 randomly selected animals that MedChemExpress Etomoxir experienced learning in the RAWM (control, n = 6; stress, n = 6). Baseline levels of corticosterone were determined from samples collected after animals had acclimated to their environment for a week but before CUS commenced. In order to see what impact CUS and the RAWM had on corticosterone, fecal samples were collected 24 hours after the last stressor and again following the long-term memory trial for the RAWM. Corticosterone levels were quantified using a commercially available Enzyme Immunoassay Kit (Assay Designs, Michigan, USA), according to the manufacturer’s instructions.Materials and Methods Ethics StatementAll experimental procedures were conducted in accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The relevant animal protocol was approved by the University of Houston Institutional Animal Care and Use Committee (protocol number 10?39).Animals and CUS ParadigmAdult male Long Evans rats (3 months old at the start of experiments) were individually housed in clear plastic cages with ad libitum food and water. Upon arrival, animals habituated for one week to the vivarium environment. CUS was administered as previously described [9,16] for 14 days. Briefly, two different daily stressors (e.g., tilted cages, vinegar-laced water, exposure to strobe light, predator odor and predator calls) as well as the timing of the stressors, were determined by a random number generator. All stressors were conducted in a room separate from where control animals were housed.HistologyOne day after the end of CUS, control (n = 9) and stress (n 1527786 = 9) animals were overdosed with anesthetic and intracardially perfused with 4 paraformaldehyde. Brains were removed and post-fixed overnight, then stored in 30 sucrose. Brains were cut into 50 mm sections on a freezing microtome and stored in cryoprotectant in 96-well microtiter plates at 220uC. To label doublecortin-positive (DCX+) cells, standard immunohistochemical procedures were used to process every sixth section throughout the rostrocaudal extent of the hippocampus. Following treatment in 0.6 hydrogen peroxide and blocking in 3 donkey serum, sections were incubated for 72 hours at 4uC in primary antibody (goat anti-DCX, Santa Cruz Biotechnology, Inc., CA, USA,.H trial were randomized, but never included the goal arm, which remained the same throughout all trials. If the rat could not find the platform within 1 minute, it was guided to and allowed to sit on the platform during the intertrial interval. During the 1-minute intertrial interval, animals remained on the platform. The 12 acquisition trials were divided into two blocks of six consecutive trials, interspersed with a 5-minute break. Following the acquisition trials, the animals underwent a short-term memory trial (30 minutes later) and a long-term memory trial (24 hours later). For each trial, latency to locate the platform and number of errors were recorded. Errors were operationally defined as anytime the animal’s entire body entered an arm that was not the goal arm, as well as anytime an animal entered the goal arm but did not find the hidden platform.Corticosterone AssessmentTo verify that CUS and learning experience were stressful, we assessed corticosterone levels, using fecal boli, since they can be obtained without stress to the animal and fecal corticosterone is highly correlated with serum corticosterone [22,23]. Fecal boli were collected from 12 randomly selected animals that experienced learning in the RAWM (control, n = 6; stress, n = 6). Baseline levels of corticosterone were determined from samples collected after animals had acclimated to their environment for a week but before CUS commenced. In order to see what impact CUS and the RAWM had on corticosterone, fecal samples were collected 24 hours after the last stressor and again following the long-term memory trial for the RAWM. Corticosterone levels were quantified using a commercially available Enzyme Immunoassay Kit (Assay Designs, Michigan, USA), according to the manufacturer’s instructions.Materials and Methods Ethics StatementAll experimental procedures were conducted in accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The relevant animal protocol was approved by the University of Houston Institutional Animal Care and Use Committee (protocol number 10?39).Animals and CUS ParadigmAdult male Long Evans rats (3 months old at the start of experiments) were individually housed in clear plastic cages with ad libitum food and water. Upon arrival, animals habituated for one week to the vivarium environment. CUS was administered as previously described [9,16] for 14 days. Briefly, two different daily stressors (e.g., tilted cages, vinegar-laced water, exposure to strobe light, predator odor and predator calls) as well as the timing of the stressors, were determined by a random number generator. All stressors were conducted in a room separate from where control animals were housed.HistologyOne day after the end of CUS, control (n = 9) and stress (n 1527786 = 9) animals were overdosed with anesthetic and intracardially perfused with 4 paraformaldehyde. Brains were removed and post-fixed overnight, then stored in 30 sucrose. Brains were cut into 50 mm sections on a freezing microtome and stored in cryoprotectant in 96-well microtiter plates at 220uC. To label doublecortin-positive (DCX+) cells, standard immunohistochemical procedures were used to process every sixth section throughout the rostrocaudal extent of the hippocampus. Following treatment in 0.6 hydrogen peroxide and blocking in 3 donkey serum, sections were incubated for 72 hours at 4uC in primary antibody (goat anti-DCX, Santa Cruz Biotechnology, Inc., CA, USA,.
]]>http://www.pi4kinhibitor.com/2017/09/26/h-trial-were-randomized-but-never-included-the-goal-arm-which/feed/0Rate complex in the oncogenic mutant p21ras continuously changes, andhttp://www.pi4kinhibitor.com/2017/09/26/rate-complex-in-the-oncogenic-mutant-p21ras-continuously-changes-and/
http://www.pi4kinhibitor.com/2017/09/26/rate-complex-in-the-oncogenic-mutant-p21ras-continuously-changes-and/#commentsTue, 26 Sep 2017 01:51:59 +0000http://www.pi4kinhibitor.com/?p=4187Rate complex in the oncogenic mutant p21ras continuously changes, and these changes in the active site would make it difficult for the GTPGDP hydrolysis reaction to occur in the mutant. Recently, Messner et al. [60] indicated that p.G13D mutated CRC cells are more sensitive to anti-EGFR treatment than codon 12-or codon 61mutated cells and the p.G13D-mutated CRC cells seem to define a less aggressive phenotype. Similarly, De Roock W et al. [26] suggested that p.G12V-mutated cells were insensitive to cetuximab, however, p.G13-mutated cells were nearly as response to cetuximab as wild-type cells. The rate of GTP-to-GDP conversion can be dramatically accelerated by an accessory protein of the guanine nucleotide activating protein (GAP) class, for example, RasGAP [61]. KRAS undergoes conformational changes when it binds GTP. This binding involves two regions of the protein?1) the switch I region and (2) the switch II region hich together form an effector loop that is responsible for controlling the specificity of the binding of STA-4783 web GTPase to its effector molecules. This conformational change in the KRAS protein affects its interactions with multiple downstream transducers, that is, the GTPase-activating protein (GAPs) that amplify the GTPase activity of KRAS [62]. In the current study, our results revealed that the conformational changes of the c.35G.A (p.G12D) mutant were significant at these sensitive sites when compared with the WT and the MT c.38G.A (p.G13D) (Figure 2). Moreover, the mutation of c.35G.A (p.G12D) may also induce additional fluctuations at these sensitive sites (Figure 3). As mentioned earlier, the switch regions I and II play important roles in the binding of regulators and effectors; therefore, we postulate that such fluctuations may promote instability in both the regions, which consequently influences the binding ability of GTPase to its effector molecules and interferes with the interactions with GAPs. As a result, impairment of the GTPase activity leads to the active form of KRAS. It should be noted that the incorporation of other amino acids in codons 12 and 13 in WT KRAS, most commonly aspartate and valine at codon 12 and aspartate at codon 13 [18], brings about the projection of larger amino acid side chains into the GDP/GTP binding pocket of the protein, thereby interfering with the steric hindrance in GTP hydrolysis [19]. Indeed, our results demonstrated by monitoring the pocket 18325633 distances between the mass center of residues 12?3 and the mass center of residues 32?4 that the GTP-binding pocket in the c.35G.A (p.G12D) mutant is more open than that of the WT and c.38G.A (p.G13D) proteins (Figure 2B). According to the molecular docking and PMF simulations for the c.38G.A (p.G13D) mutant-GTP binding, the distribution of docking scores (Figure 4) and the simulated free EHop-016 biological activity energy profile (green curve in Figure 5) are also similar to that of the wild-type KRAS-GTP binding. The data obtained from the molecular docking, MD and PMF simulations indicate that the binding of GTP with the c.35G.A (p.G12D) mutant is less favorable compared with that of GTP with wild-type KRAS or the c.38G.A (p.G13D) mutant. Based on this observation, it is reasonable to hypothesize that c.38G.A (p.G13D) is similar to wild-type KRAS, and thereby the RAS-GTP hydrolysis reactions are preserved. By contrast, the KRAS mutation in codon 12 may impair the hydrolysis of GTP, leading the KRAS protein to take a permanent form. Our data make sense in light of th.Rate complex in the oncogenic mutant p21ras continuously changes, and these changes in the active site would make it difficult for the GTPGDP hydrolysis reaction to occur in the mutant. Recently, Messner et al. [60] indicated that p.G13D mutated CRC cells are more sensitive to anti-EGFR treatment than codon 12-or codon 61mutated cells and the p.G13D-mutated CRC cells seem to define a less aggressive phenotype. Similarly, De Roock W et al. [26] suggested that p.G12V-mutated cells were insensitive to cetuximab, however, p.G13-mutated cells were nearly as response to cetuximab as wild-type cells. The rate of GTP-to-GDP conversion can be dramatically accelerated by an accessory protein of the guanine nucleotide activating protein (GAP) class, for example, RasGAP [61]. KRAS undergoes conformational changes when it binds GTP. This binding involves two regions of the protein?1) the switch I region and (2) the switch II region hich together form an effector loop that is responsible for controlling the specificity of the binding of GTPase to its effector molecules. This conformational change in the KRAS protein affects its interactions with multiple downstream transducers, that is, the GTPase-activating protein (GAPs) that amplify the GTPase activity of KRAS [62]. In the current study, our results revealed that the conformational changes of the c.35G.A (p.G12D) mutant were significant at these sensitive sites when compared with the WT and the MT c.38G.A (p.G13D) (Figure 2). Moreover, the mutation of c.35G.A (p.G12D) may also induce additional fluctuations at these sensitive sites (Figure 3). As mentioned earlier, the switch regions I and II play important roles in the binding of regulators and effectors; therefore, we postulate that such fluctuations may promote instability in both the regions, which consequently influences the binding ability of GTPase to its effector molecules and interferes with the interactions with GAPs. As a result, impairment of the GTPase activity leads to the active form of KRAS. It should be noted that the incorporation of other amino acids in codons 12 and 13 in WT KRAS, most commonly aspartate and valine at codon 12 and aspartate at codon 13 [18], brings about the projection of larger amino acid side chains into the GDP/GTP binding pocket of the protein, thereby interfering with the steric hindrance in GTP hydrolysis [19]. Indeed, our results demonstrated by monitoring the pocket 18325633 distances between the mass center of residues 12?3 and the mass center of residues 32?4 that the GTP-binding pocket in the c.35G.A (p.G12D) mutant is more open than that of the WT and c.38G.A (p.G13D) proteins (Figure 2B). According to the molecular docking and PMF simulations for the c.38G.A (p.G13D) mutant-GTP binding, the distribution of docking scores (Figure 4) and the simulated free energy profile (green curve in Figure 5) are also similar to that of the wild-type KRAS-GTP binding. The data obtained from the molecular docking, MD and PMF simulations indicate that the binding of GTP with the c.35G.A (p.G12D) mutant is less favorable compared with that of GTP with wild-type KRAS or the c.38G.A (p.G13D) mutant. Based on this observation, it is reasonable to hypothesize that c.38G.A (p.G13D) is similar to wild-type KRAS, and thereby the RAS-GTP hydrolysis reactions are preserved. By contrast, the KRAS mutation in codon 12 may impair the hydrolysis of GTP, leading the KRAS protein to take a permanent form. Our data make sense in light of th.
]]>http://www.pi4kinhibitor.com/2017/09/26/rate-complex-in-the-oncogenic-mutant-p21ras-continuously-changes-and/feed/0Ons were performed by one-way analysis of variance (ANOVA) with post-hochttp://www.pi4kinhibitor.com/2017/09/26/ons-were-performed-by-one-way-analysis-of-variance-anova-with-post-hoc/
http://www.pi4kinhibitor.com/2017/09/26/ons-were-performed-by-one-way-analysis-of-variance-anova-with-post-hoc/#commentsTue, 26 Sep 2017 01:33:43 +0000http://www.pi4kinhibitor.com/?p=4185Ons were performed by one-way analysis of variance (ANOVA) with post-hoc Bonferroni’s test. A value of p,0.05 was considered statistically significant. All data are expressed as the mean 6 S.D.Immunohistochemistry of Sectioned PreparationsThe rectum including an anastomotic site was fixed with 4 paraformaldehyde at 4uC, and embedded in paraffin. Consecutive 4 mm sections were cut from each block. Immunostaining was performed by treatment with pepsin (DAKO Corp., Carpinteria, CA, USA) for 20 min at room temperature for NF, DLX2, GFP and GFAP. After endogenous peroxidase blockade with 3 H2O2-methanol for 15 min, specimens were rinsed with PBS and incubated with a primary antibody diluted with Washing SolutionResultsIn the current study, we obtained the first in vivo images of enteric neurons and nerve fibers in the 23115181 mucosa, submucosa,Daprodustat Figure 3. A stereomicroscopic image including the observed site shown in Figure 4. A. The thick granulation tissue at the anastomotic region in a mouse that was treated with MOS solution for 1 week after anastomosis ASA-404 surgery. An area in the square (a) corresponds to an area in the square (a) in Figure 4. B. A microscopic image of a longitudinal section, prepared following fixation, that was taken along the line (b) indicated in panel A. doi:10.1371/journal.pone.0054814.gFigure 4. Immunohistochemical image for anti-neurofilament (NF) antibody of a whole mount preparation of the same intestine shown in Figure 5. A corresponds to Figure 5A (the image by 2PM). *, A knot of thread in the area between two-dotted lines indicates the anastomotic area. The granulation tissue was removed to allow for laser penetration. Normal myenteric plexus in the intact oral and anal sites are visible, but nerve cells and fibers are not visible in the anastomotic region because of the thickness of the anastomotic area. doi:10.1371/journal.pone.0054814.gIn Vivo Imaging of Enteric NeurogenesisFigure 6. Images of anastomosis of the ileum in an SB-207266 (SB) plus MOS treated mouse. SB plus MOS treatment was performed for one week. A. Images stacked in the Z axis with a total depth of 200 – 300 mm. A . image 38 mm deep to the serosa surface in area (a) in A. A . image 71 mm deep to the serosa surface in area (b) in A. Circles indicate aggregates of small non-neuronal cells (A and b), respectively. doi:10.1371/journal.pone.0054814.gFigure 5. Images of anastomotic region of the terminal ileum in a MOS-treated mouse. The dotted lines indicates the anastomosis site. Around the knot of thread we obtained each image from 9 visual fields. A. Images stacked with Z axis to a total depth of 200?00 mm. A?a. image 42 mm deep to the serosa surface in area (a) in A. A ‘. image 174 mm deep to the serosa surface in the same area (a) in A. A . 44 mm deep to the serosa surface in area (b) in A. A ‘. image 101 mm deep to the serosa surface in the same area (b) in A. Arrows indicate nerve cells in A ‘, b and b’, and arrowheads indicate nerve fibers in A , a’, b and b’, and circles indicate ganglion-like clusters of neurons in A , b and b’, respectively. B. Number of neurons in each field (size: 310 mm6310 mm) around the knot. C. Newborn nerve cells formed ganglion structures indicated by circles. These were enlarged from the images shown in A?b’ and i. doi:10.1371/journal.pone.0054814.gsubmucosal and myenteric plexuses, and circular and longitudinal muscles of the terminal ileum (Figure 2). We initially confirmed that enteric neurons could be imaged in.Ons were performed by one-way analysis of variance (ANOVA) with post-hoc Bonferroni’s test. A value of p,0.05 was considered statistically significant. All data are expressed as the mean 6 S.D.Immunohistochemistry of Sectioned PreparationsThe rectum including an anastomotic site was fixed with 4 paraformaldehyde at 4uC, and embedded in paraffin. Consecutive 4 mm sections were cut from each block. Immunostaining was performed by treatment with pepsin (DAKO Corp., Carpinteria, CA, USA) for 20 min at room temperature for NF, DLX2, GFP and GFAP. After endogenous peroxidase blockade with 3 H2O2-methanol for 15 min, specimens were rinsed with PBS and incubated with a primary antibody diluted with Washing SolutionResultsIn the current study, we obtained the first in vivo images of enteric neurons and nerve fibers in the 23115181 mucosa, submucosa,Figure 3. A stereomicroscopic image including the observed site shown in Figure 4. A. The thick granulation tissue at the anastomotic region in a mouse that was treated with MOS solution for 1 week after anastomosis surgery. An area in the square (a) corresponds to an area in the square (a) in Figure 4. B. A microscopic image of a longitudinal section, prepared following fixation, that was taken along the line (b) indicated in panel A. doi:10.1371/journal.pone.0054814.gFigure 4. Immunohistochemical image for anti-neurofilament (NF) antibody of a whole mount preparation of the same intestine shown in Figure 5. A corresponds to Figure 5A (the image by 2PM). *, A knot of thread in the area between two-dotted lines indicates the anastomotic area. The granulation tissue was removed to allow for laser penetration. Normal myenteric plexus in the intact oral and anal sites are visible, but nerve cells and fibers are not visible in the anastomotic region because of the thickness of the anastomotic area. doi:10.1371/journal.pone.0054814.gIn Vivo Imaging of Enteric NeurogenesisFigure 6. Images of anastomosis of the ileum in an SB-207266 (SB) plus MOS treated mouse. SB plus MOS treatment was performed for one week. A. Images stacked in the Z axis with a total depth of 200 – 300 mm. A . image 38 mm deep to the serosa surface in area (a) in A. A . image 71 mm deep to the serosa surface in area (b) in A. Circles indicate aggregates of small non-neuronal cells (A and b), respectively. doi:10.1371/journal.pone.0054814.gFigure 5. Images of anastomotic region of the terminal ileum in a MOS-treated mouse. The dotted lines indicates the anastomosis site. Around the knot of thread we obtained each image from 9 visual fields. A. Images stacked with Z axis to a total depth of 200?00 mm. A?a. image 42 mm deep to the serosa surface in area (a) in A. A ‘. image 174 mm deep to the serosa surface in the same area (a) in A. A . 44 mm deep to the serosa surface in area (b) in A. A ‘. image 101 mm deep to the serosa surface in the same area (b) in A. Arrows indicate nerve cells in A ‘, b and b’, and arrowheads indicate nerve fibers in A , a’, b and b’, and circles indicate ganglion-like clusters of neurons in A , b and b’, respectively. B. Number of neurons in each field (size: 310 mm6310 mm) around the knot. C. Newborn nerve cells formed ganglion structures indicated by circles. These were enlarged from the images shown in A?b’ and i. doi:10.1371/journal.pone.0054814.gsubmucosal and myenteric plexuses, and circular and longitudinal muscles of the terminal ileum (Figure 2). We initially confirmed that enteric neurons could be imaged in.
]]>http://www.pi4kinhibitor.com/2017/09/26/ons-were-performed-by-one-way-analysis-of-variance-anova-with-post-hoc/feed/0Latelet accumulation to collagen surface concentration (Fig. 2). Whole blood was perfusedhttp://www.pi4kinhibitor.com/2017/09/26/latelet-accumulation-to-collagen-surface-concentration-fig-2-whole-blood-was-perfused/
http://www.pi4kinhibitor.com/2017/09/26/latelet-accumulation-to-collagen-surface-concentration-fig-2-whole-blood-was-perfused/#commentsTue, 26 Sep 2017 01:23:41 +0000http://www.pi4kinhibitor.com/?p=4183Latelet accumulation to collagen surface concentration (Fig. 2). Whole blood was perfused over each surface at 300 s21. momelotinib platelet accumulation as measured by SC was significantly lower (p,0.01) on the 5?0 mg/mL substrates than the higher collagen concentrations (n = 21). There was noVariability in Microfluidic Flow AssaysTable 1. Characteristics of the cohort of donors.Total number of donors Women Oral Contraception Age, mean 6 stdev (range) Hematocrit, mean 6 stdev (range) Combined Women Men Platelet count (plt/mL), mean 6 stdev (range) Combined Women Men CY5-SE plasma VWF (IU/dL), mean 6 stdev (range) Combined Women Men doi:10.1371/journal.pone.0054680.t104 60 (58 ) 13 (21 of women) 32.5611.0 (21?4)43.964.8 (27.0?4.1) 41.564.2 (27.0?6.9) 47.862.9 (44.0?4.1)311,000656,000 (211,000?03,000) 321,000664,000 (211,000?03,000) 291,000630,000 (255,000?70,000)87.9635.1 (26.3?78.2) 97.3630.4 (38.5?78.2) 73.4630.1 (26.3?51.4)statistical difference in SC over the range of 50?000 mg/ml, suggesting that these surface concentrations of collagen exceed the surface concentration of collagen receptors on platelets. Therefore, differences between donors can be attributed to composition of plasma proteins such as VWF and collagen and VWF receptor density. We chose 100 mg/mL for all subsequent experiments because this a common concentration used for type 1 fibrillar collagen in flow assay studies [16].MFA ReproducibilityTo quantify the reproducibility of the MFA, we tested 18325633 five donors on four separate days over a two-week interval (Table 2). Phlebotomy was performed at the same time of day for each draw. The average coefficient of variation in SC was less than 0.15 at 150, 300, and 750 s21, but larger at 1500 s21 (0.45). We attribute the high CV for 1500 s21 to the relatively low levels of platelet accumulation at this shear rate, rather than as an indication of a systematic source of variability within the assay. Donor 3 had very low binding, including insignificant platelet adhesion at 750 s21, compared to the other donors. However, this behavior was reproducible for each test and indicative of the low binder group observed in the larger 1655472 cohort (described in the next section). While the intra-donor variability is low, the inter-donor variability is quite high as indicated by the large standard deviation in SC between the five donors. A large cohort was recruited to identify the source of this variability.Characteristics of Platelet Accumulation in the MFA in a Large Cohort of Normal DonorsFifty normal donors were recruited and their platelet accumulation on type 1 collagen (100 mg/mL) was measured at 150, 300, 750 and 1500 s21. Fig. 3 shows representative images before and after image processing at the end of a 5 min assay. Platelet SC peaked at 300 s21 and was lowest at 1500 s21 (Fig. 4A). The rate of platelet accumulation (VPLT) was lowest at 150 s21 and different (p,0.01) than the other three shear rates (Fig. 4B). There was no difference in VPLT between the higher three shear rates. The lag time (LagT) was similar at 150 s21 and 300 s21, and significantly higher (p,0.01) at 750 s21 and 1500 s21 (Fig. 4C). The differences LagT between the low and high shear rates are associated with the time required for a significant amount of VWF to bind to the collagen (see The lag time for platelet accumulation at high shear rates is due to adsorption of plasma proteins below).Figure 2. Sensitivity of platelet accumulation to collagen surface density. Type 1 fibrillar co.Latelet accumulation to collagen surface concentration (Fig. 2). Whole blood was perfused over each surface at 300 s21. Platelet accumulation as measured by SC was significantly lower (p,0.01) on the 5?0 mg/mL substrates than the higher collagen concentrations (n = 21). There was noVariability in Microfluidic Flow AssaysTable 1. Characteristics of the cohort of donors.Total number of donors Women Oral Contraception Age, mean 6 stdev (range) Hematocrit, mean 6 stdev (range) Combined Women Men Platelet count (plt/mL), mean 6 stdev (range) Combined Women Men Plasma VWF (IU/dL), mean 6 stdev (range) Combined Women Men doi:10.1371/journal.pone.0054680.t104 60 (58 ) 13 (21 of women) 32.5611.0 (21?4)43.964.8 (27.0?4.1) 41.564.2 (27.0?6.9) 47.862.9 (44.0?4.1)311,000656,000 (211,000?03,000) 321,000664,000 (211,000?03,000) 291,000630,000 (255,000?70,000)87.9635.1 (26.3?78.2) 97.3630.4 (38.5?78.2) 73.4630.1 (26.3?51.4)statistical difference in SC over the range of 50?000 mg/ml, suggesting that these surface concentrations of collagen exceed the surface concentration of collagen receptors on platelets. Therefore, differences between donors can be attributed to composition of plasma proteins such as VWF and collagen and VWF receptor density. We chose 100 mg/mL for all subsequent experiments because this a common concentration used for type 1 fibrillar collagen in flow assay studies [16].MFA ReproducibilityTo quantify the reproducibility of the MFA, we tested 18325633 five donors on four separate days over a two-week interval (Table 2). Phlebotomy was performed at the same time of day for each draw. The average coefficient of variation in SC was less than 0.15 at 150, 300, and 750 s21, but larger at 1500 s21 (0.45). We attribute the high CV for 1500 s21 to the relatively low levels of platelet accumulation at this shear rate, rather than as an indication of a systematic source of variability within the assay. Donor 3 had very low binding, including insignificant platelet adhesion at 750 s21, compared to the other donors. However, this behavior was reproducible for each test and indicative of the low binder group observed in the larger 1655472 cohort (described in the next section). While the intra-donor variability is low, the inter-donor variability is quite high as indicated by the large standard deviation in SC between the five donors. A large cohort was recruited to identify the source of this variability.Characteristics of Platelet Accumulation in the MFA in a Large Cohort of Normal DonorsFifty normal donors were recruited and their platelet accumulation on type 1 collagen (100 mg/mL) was measured at 150, 300, 750 and 1500 s21. Fig. 3 shows representative images before and after image processing at the end of a 5 min assay. Platelet SC peaked at 300 s21 and was lowest at 1500 s21 (Fig. 4A). The rate of platelet accumulation (VPLT) was lowest at 150 s21 and different (p,0.01) than the other three shear rates (Fig. 4B). There was no difference in VPLT between the higher three shear rates. The lag time (LagT) was similar at 150 s21 and 300 s21, and significantly higher (p,0.01) at 750 s21 and 1500 s21 (Fig. 4C). The differences LagT between the low and high shear rates are associated with the time required for a significant amount of VWF to bind to the collagen (see The lag time for platelet accumulation at high shear rates is due to adsorption of plasma proteins below).Figure 2. Sensitivity of platelet accumulation to collagen surface density. Type 1 fibrillar co.
]]>http://www.pi4kinhibitor.com/2017/09/26/latelet-accumulation-to-collagen-surface-concentration-fig-2-whole-blood-was-perfused/feed/0Index. aAll 8 candidate HKGs showed strong correlation (correlation coefficient r valuehttp://www.pi4kinhibitor.com/2017/09/25/index-aall-8-candidate-hkgs-showed-strong-correlation-correlation-coefficient-r-value/
http://www.pi4kinhibitor.com/2017/09/25/index-aall-8-candidate-hkgs-showed-strong-correlation-correlation-coefficient-r-value/#commentsMon, 25 Sep 2017 06:55:18 +0000http://www.pi4kinhibitor.com/?p=4181Index. aAll 8 candidate HKGs showed strong correlation (correlation coefficient r value from 0.69 to 0.93) and were combined into an index, which was then used to compute the correlation between each HKG and the index. doi:10.1371/journal.pone.0048367.gunstimulated CD4+ T cells were studied. It is possible that PPIA level is low in resting CD4+ T cells. Upon allergen stimulation, such as in acute asthmatics or chronic asthmatics with continuous allergen exposure, PPIA JSH-23 manufacturer expression would be higher than normal. This phenomenon was seen previously with other chemoattractants such as eotaxin, RANTES, MIP-1a, and MCP-1 [23,24,25]. Our previous study identified PPIA as a stable expressed HKG in airway epithelial cells [26], this paper has provided helpful information to a dozen of studies since its publication (citations from 11967625 Google Scholar). Several publications used PPIA as a HKG to normalize the expression levels of target genes and found meaningful differential expressions of target genes [27,28], Current study identified B2M and RPLP0 as the most optimal HKGs in gene expression studies involving human blood CD4+ T Table 4. Primer sequences for housekeeping genes.cells derived from normal subjects and asthmatics with and without depression. The different results from the two studies may be explained by the fact that the cell types in the two studies were different and our results have also strengthened the importance of optimal HKGs selection before performing any qRT-PCR in different disease conditions. Since asthma with depression have been considered to influence the disease process of asthma certainly, JNJ-7777120 exploring the underlying pathophysiological mechanisms is necessary. However, before we determine the molecular basis, selecting optimal HKGs is the first and crucial step.ConclusionsTo our knowledge, this is the first study to identify the most stable HKGs in CD4+ T cells and depressive/non-depressive asthmatic disease status. B2M and RPLP0 were identified as the most optimal combination of HKGs in gene expression studies involving human blood CD4+ T cells derived from normal, depressive asthmatics and non-depressive asthmatics. Moreover, the present findings question the suitability of the PPIA gene as the HKG for such studies due to its significantly lower expression levels in asthmatic CD4+ T cells. Furthermore, careful comparison of the gene expression profiles of purified CD4+ T cells based on information from this study will further elucidate the molecular basis of the incidence and development of asthma with or without depression.Symbol RN28S1 RPLP0 ACTB PPIA GAPDH PGK1 B2M GUSB RPL13AForward primer CTCCCACTTATTCTACACCT CTGGAAGTCCAACTACTTCCT GAAGATCAAGATCATTGCTCCT TCCTGGCATCTTGTCCAT AAGCTCATTTCCTGGTATGACA GCCACTTGCTGTGCCAAATG CTATCCAGCGTACTCCAAAG CCAGTTTGAGAACTGGTATAAG CTTTCCTCCGCAAGCGGATReverse primer CCACTGTCCCTACCTACTAT 15857111 CATCATGGTGTTCTTGCCCAT TACTCCTGCTTGCTGATCCA TGCTGGTCTTGCCATTCCT TCTTACTCCTTGGAGGCCATGT CCCAGGAAGGACTTTACCTT GAAAGACCAGTCCTTGCTGA CTGGTACTCTTCAGTGAACAT CCACCATCCGCTTTTTCTTAcknowledgmentsWe thank Dr. Ya-Jing Meng, a psychiatrist for evaluation the psychological conditions of these subjects, Yan He and Qing-Jie Xia for helping experiment technology; and all of the subjects for their participation.doi:10.1371/journal.pone.0048367.tSelection of Suitable Housekeeping GenesFigure 3. Ranking the housekeeping genes (HKGs) according to their expression stability M determined using geNorm. A stepwise exclusion of the least.Index. aAll 8 candidate HKGs showed strong correlation (correlation coefficient r value from 0.69 to 0.93) and were combined into an index, which was then used to compute the correlation between each HKG and the index. doi:10.1371/journal.pone.0048367.gunstimulated CD4+ T cells were studied. It is possible that PPIA level is low in resting CD4+ T cells. Upon allergen stimulation, such as in acute asthmatics or chronic asthmatics with continuous allergen exposure, PPIA expression would be higher than normal. This phenomenon was seen previously with other chemoattractants such as eotaxin, RANTES, MIP-1a, and MCP-1 [23,24,25]. Our previous study identified PPIA as a stable expressed HKG in airway epithelial cells [26], this paper has provided helpful information to a dozen of studies since its publication (citations from 11967625 Google Scholar). Several publications used PPIA as a HKG to normalize the expression levels of target genes and found meaningful differential expressions of target genes [27,28], Current study identified B2M and RPLP0 as the most optimal HKGs in gene expression studies involving human blood CD4+ T Table 4. Primer sequences for housekeeping genes.cells derived from normal subjects and asthmatics with and without depression. The different results from the two studies may be explained by the fact that the cell types in the two studies were different and our results have also strengthened the importance of optimal HKGs selection before performing any qRT-PCR in different disease conditions. Since asthma with depression have been considered to influence the disease process of asthma certainly, exploring the underlying pathophysiological mechanisms is necessary. However, before we determine the molecular basis, selecting optimal HKGs is the first and crucial step.ConclusionsTo our knowledge, this is the first study to identify the most stable HKGs in CD4+ T cells and depressive/non-depressive asthmatic disease status. B2M and RPLP0 were identified as the most optimal combination of HKGs in gene expression studies involving human blood CD4+ T cells derived from normal, depressive asthmatics and non-depressive asthmatics. Moreover, the present findings question the suitability of the PPIA gene as the HKG for such studies due to its significantly lower expression levels in asthmatic CD4+ T cells. Furthermore, careful comparison of the gene expression profiles of purified CD4+ T cells based on information from this study will further elucidate the molecular basis of the incidence and development of asthma with or without depression.Symbol RN28S1 RPLP0 ACTB PPIA GAPDH PGK1 B2M GUSB RPL13AForward primer CTCCCACTTATTCTACACCT CTGGAAGTCCAACTACTTCCT GAAGATCAAGATCATTGCTCCT TCCTGGCATCTTGTCCAT AAGCTCATTTCCTGGTATGACA GCCACTTGCTGTGCCAAATG CTATCCAGCGTACTCCAAAG CCAGTTTGAGAACTGGTATAAG CTTTCCTCCGCAAGCGGATReverse primer CCACTGTCCCTACCTACTAT 15857111 CATCATGGTGTTCTTGCCCAT TACTCCTGCTTGCTGATCCA TGCTGGTCTTGCCATTCCT TCTTACTCCTTGGAGGCCATGT CCCAGGAAGGACTTTACCTT GAAAGACCAGTCCTTGCTGA CTGGTACTCTTCAGTGAACAT CCACCATCCGCTTTTTCTTAcknowledgmentsWe thank Dr. Ya-Jing Meng, a psychiatrist for evaluation the psychological conditions of these subjects, Yan He and Qing-Jie Xia for helping experiment technology; and all of the subjects for their participation.doi:10.1371/journal.pone.0048367.tSelection of Suitable Housekeeping GenesFigure 3. Ranking the housekeeping genes (HKGs) according to their expression stability M determined using geNorm. A stepwise exclusion of the least.
]]>http://www.pi4kinhibitor.com/2017/09/25/index-aall-8-candidate-hkgs-showed-strong-correlation-correlation-coefficient-r-value/feed/0S in food intake. Power analysis indicates that to determine withhttp://www.pi4kinhibitor.com/2017/09/25/s-in-food-intake-power-analysis-indicates-that-to-determine-with/
http://www.pi4kinhibitor.com/2017/09/25/s-in-food-intake-power-analysis-indicates-that-to-determine-with/#commentsMon, 25 Sep 2017 06:49:18 +0000http://www.pi4kinhibitor.com/?p=4179S in food intake. Power analysis indicates that to determine with 95 certainty whether this 3.7 difference in food intake was I-BRD9 biological activity significant would require 126 mice of each genotype. As, over a more prolonged period, a difference in 3 days-accumulated food intake of as little as 3.7 is likely to be able alter body Sapanisertib site weight and composition [23], in this study, we cannot exclude such a small difference being present. As the timing of food intake can influence energy storage independently of total intake [24], we also measured food intakeafter fasting, as well as during the light and dark phases in all animals (Figs 3B, 3C, 3D). However, there was no difference between knockout and control mice of either sex with respect to re-feeding after a 24-hour fast (Fig. 3B, p = 0.8 for both sexes). Additionally, there were no significant differences in the pattern of food intake in the light and dark phase between male and female MIC-12/2 and control mice (Fig. 3C, 3D).Female but not Male MIC-12/2 Mice have Lower Total Energy ExpenditureTo further investigate possible mechanisms underlying the increases in body weight and adiposity of male and female MIC12/2 versus MIC-1+/+ mice, we compared their respiratory exchange ratio (RER), energy expenditure and physical activity (Figs 4 and 5). The increased body weight and adiposity of MIC12/2 animals does not appear to result from differential use of lipids versus carbohydrate as oxidative fuel sources as there was no difference in RER between genotypes (Fig. 4A, 5A). Female mice, MIC-12/2 animals exhibit significantly lower energy expenditureMIC-1/GDF15 Regulates Appetite and Body WeightFigure 6. Major contribution to genotypic difference in total EE was basal metabolism. Correlation between physical activity and EE was based on average values collected over 24 h. Each point represents data collected in 1-h intervals from the (A) male MIC-12/2 and control mice (Trend line equation: MIC-12/2 y = 12932x ?375 R2 = 0.8705, control y = 18893x ?637 R2 = 0.8813) and (B) female MIC-12/2 and control mice (Trend line equation: MIC-12/2 y = 18517x ?851 R2 = 0.8796, control y = 12326x ?628 R2 = 0.8261). Basal metabolic rate is determined using the function from the trend line and extrapolating to set the physical activity to zero. No significant difference in basal metabolic rate between the male genotypes (0.3560.01 vs 0.3460.02, respectively, p = 0.23, n = 15/group). Basal metabolic rate was significantly lower in the female MIC-12/2 mice compared to control (0.3760.02 vs 0.2960.01, respectively, p,0.01, n = 9/group). Data are means 6 SE. doi:10.1371/journal.pone.0055174.gFigure 7. Physiological levels of human MIC-1/GDF15 reduce weight and food intake in mice. Male MIC-12/2 and MIC-1+/+ mice were infused with human MIC-1/GDF15 (1ug/20gBW/d) or vehicle via osmotic mini-pump. Food intake, body weight and serum levels of human MIC-1/ GDF15 were measured on day 5 of infusion. (A) MIC-1/GDF15-treated MIC-12/2 mice had an average serum MIC-1/GDF15 level of 643667 pg/ml and weighed 95.8660.77 18334597 of their starting body weight whilst vehicle-treated mice weighed 102.360.75 of their starting weight (n = 6/group, p,0.01 unpaired t-test). (B) MIC-1/GDF15-treated MIC-1+/+ mice had an average serum MIC-1/GDF15 level of 576645 pg/ml and weighed 99.8660.47 of their starting weight whilst vehicle-treated mice weighed 10260.52 (n = 14, p = 0.01 unpaired t-test). This decreased body weight in both genotypes was associated with reduc.S in food intake. Power analysis indicates that to determine with 95 certainty whether this 3.7 difference in food intake was significant would require 126 mice of each genotype. As, over a more prolonged period, a difference in 3 days-accumulated food intake of as little as 3.7 is likely to be able alter body weight and composition [23], in this study, we cannot exclude such a small difference being present. As the timing of food intake can influence energy storage independently of total intake [24], we also measured food intakeafter fasting, as well as during the light and dark phases in all animals (Figs 3B, 3C, 3D). However, there was no difference between knockout and control mice of either sex with respect to re-feeding after a 24-hour fast (Fig. 3B, p = 0.8 for both sexes). Additionally, there were no significant differences in the pattern of food intake in the light and dark phase between male and female MIC-12/2 and control mice (Fig. 3C, 3D).Female but not Male MIC-12/2 Mice have Lower Total Energy ExpenditureTo further investigate possible mechanisms underlying the increases in body weight and adiposity of male and female MIC12/2 versus MIC-1+/+ mice, we compared their respiratory exchange ratio (RER), energy expenditure and physical activity (Figs 4 and 5). The increased body weight and adiposity of MIC12/2 animals does not appear to result from differential use of lipids versus carbohydrate as oxidative fuel sources as there was no difference in RER between genotypes (Fig. 4A, 5A). Female mice, MIC-12/2 animals exhibit significantly lower energy expenditureMIC-1/GDF15 Regulates Appetite and Body WeightFigure 6. Major contribution to genotypic difference in total EE was basal metabolism. Correlation between physical activity and EE was based on average values collected over 24 h. Each point represents data collected in 1-h intervals from the (A) male MIC-12/2 and control mice (Trend line equation: MIC-12/2 y = 12932x ?375 R2 = 0.8705, control y = 18893x ?637 R2 = 0.8813) and (B) female MIC-12/2 and control mice (Trend line equation: MIC-12/2 y = 18517x ?851 R2 = 0.8796, control y = 12326x ?628 R2 = 0.8261). Basal metabolic rate is determined using the function from the trend line and extrapolating to set the physical activity to zero. No significant difference in basal metabolic rate between the male genotypes (0.3560.01 vs 0.3460.02, respectively, p = 0.23, n = 15/group). Basal metabolic rate was significantly lower in the female MIC-12/2 mice compared to control (0.3760.02 vs 0.2960.01, respectively, p,0.01, n = 9/group). Data are means 6 SE. doi:10.1371/journal.pone.0055174.gFigure 7. Physiological levels of human MIC-1/GDF15 reduce weight and food intake in mice. Male MIC-12/2 and MIC-1+/+ mice were infused with human MIC-1/GDF15 (1ug/20gBW/d) or vehicle via osmotic mini-pump. Food intake, body weight and serum levels of human MIC-1/ GDF15 were measured on day 5 of infusion. (A) MIC-1/GDF15-treated MIC-12/2 mice had an average serum MIC-1/GDF15 level of 643667 pg/ml and weighed 95.8660.77 18334597 of their starting body weight whilst vehicle-treated mice weighed 102.360.75 of their starting weight (n = 6/group, p,0.01 unpaired t-test). (B) MIC-1/GDF15-treated MIC-1+/+ mice had an average serum MIC-1/GDF15 level of 576645 pg/ml and weighed 99.8660.47 of their starting weight whilst vehicle-treated mice weighed 10260.52 (n = 14, p = 0.01 unpaired t-test). This decreased body weight in both genotypes was associated with reduc.
]]>http://www.pi4kinhibitor.com/2017/09/25/s-in-food-intake-power-analysis-indicates-that-to-determine-with/feed/0Study. U251 cells (56106) were injected into the right hind flank subcutaneously.http://www.pi4kinhibitor.com/2017/09/25/study-u251-cells-56106-were-injected-into-the-right-hind-flank-subcutaneously/
http://www.pi4kinhibitor.com/2017/09/25/study-u251-cells-56106-were-injected-into-the-right-hind-flank-subcutaneously/#commentsMon, 25 Sep 2017 06:42:19 +0000http://www.pi4kinhibitor.com/?p=4177Study. U251 cells (56106) were injected into the right hind flank subcutaneously. When the tumors reached a volume of ,150 mm3 they were randomized into one of the two groups. One group received EGF-SubA (125 mg/kg; n = 6) in sterile PBS (100 ml) and the control group received the same volume of PBSTargeting the UPR in Glioblastoma with EGF-SubAFigure 3. The influence of SubA and EGF-SubA on glioma cell survival. A clonogenic assay was performed to study the GSK2879552 custom synthesis cytoxicity of SubA and EGF-SubA in U251 (A), T98G (B) and U87 cells (C). Cells were seeded as single cell suspensions in six well culture plates, allowed to adhere, and treated with the stated GW0742 web concentrations of SubA or EGF-SubA for 24 h. Plates were then replaced with fresh culture media and surviving fractions were calculated 10 to 14 d following treatment. Cell survival was significantly different between SubA and EGF SubA treatment in U251 (p,0.0001) and T98G (p,0.0001 at concentrations 0.5 pM) and not significant in U87 cells (p = 0.2112). (D) Immunoblotting of total cellular protein from U251 cells treated with EGF-SubA at the stated concentrations for 24 h demonstrates EGF-SubA induced apoptosis, as determined by cleaved caspase 3. Each figure is a representative of three independent experiments. doi:10.1371/journal.pone.0052265.galone (n = 6) subcutaneously behind the neck. A total of three doses were delivered every other day. The tumor volume (L x W x W/2) and mice weight were measured every other day. The mice were sacrificed when the tumor volume reached 1000 mm3. Prior to their tumors reaching this size, mice were euthanatized ifthey experienced an evidence of suffering, including inactivity, labored breathing, interfere with posture, locomotion or feeding, weight loss of more than 10 , or ulceration of the tumor. Mice were euthanatized by carbon dioxide.Figure 4. EGF-SubA enhances anti-tumor activity of temozolomide and ionizing radiation. A clonogenic assay was performed to evaluate the potential of EGF-SubA to enhance temozolomide (A) (statistically significant p,0.0001) and radiation-induced (B) cytotoxicity (statistically significant p,0.0024). U251 cells were seeded in six well culture plates and exposed to 1 pM of EGF-SubA 16 h prior to the addition of temozolomide or radiation exposure. Fresh media was then replaced in the culture plates after 8 h, and surviving fractions were calculated 10 to 14 d following treatment, normalizing for the individual cytotoxicity of EGF-SubA. Each figure is a representative of three independent experiments. doi:10.1371/journal.pone.0052265.gTargeting the UPR in Glioblastoma with EGF-SubAFigure 5. Acidic pH activates the UPR pathway and enhances EGF-SubA cytotoxicity. U251 cells grown in RPMI media whose pH was adjusted to 6.7 and 7.0 with 1N HCl for 3 passages prior to performing experiments demonstrated UPR activation, as determined by PERK phosphorylation (A; pPERK), Xbp1 splicing and increased GRP78 transcription (B). (C) To determine if cells grown in acidic conditions influenced EGFSubA cytotoxicity, a clonogenic assay was performed with U251 cells grown in normal (pH 7.4) or acidic (pH 6.7) conditions at the stated concentrations. Cell survival was significantly different between cells grown in normal and acidic pH at higher doses of EGF SubA (p,0.0001 at 2.5 18325633 pM). Each figure is a representative of three independent experiments. doi:10.1371/journal.pone.0052265.gxCELLigenceCell proliferation under normal and treated condit.Study. U251 cells (56106) were injected into the right hind flank subcutaneously. When the tumors reached a volume of ,150 mm3 they were randomized into one of the two groups. One group received EGF-SubA (125 mg/kg; n = 6) in sterile PBS (100 ml) and the control group received the same volume of PBSTargeting the UPR in Glioblastoma with EGF-SubAFigure 3. The influence of SubA and EGF-SubA on glioma cell survival. A clonogenic assay was performed to study the cytoxicity of SubA and EGF-SubA in U251 (A), T98G (B) and U87 cells (C). Cells were seeded as single cell suspensions in six well culture plates, allowed to adhere, and treated with the stated concentrations of SubA or EGF-SubA for 24 h. Plates were then replaced with fresh culture media and surviving fractions were calculated 10 to 14 d following treatment. Cell survival was significantly different between SubA and EGF SubA treatment in U251 (p,0.0001) and T98G (p,0.0001 at concentrations 0.5 pM) and not significant in U87 cells (p = 0.2112). (D) Immunoblotting of total cellular protein from U251 cells treated with EGF-SubA at the stated concentrations for 24 h demonstrates EGF-SubA induced apoptosis, as determined by cleaved caspase 3. Each figure is a representative of three independent experiments. doi:10.1371/journal.pone.0052265.galone (n = 6) subcutaneously behind the neck. A total of three doses were delivered every other day. The tumor volume (L x W x W/2) and mice weight were measured every other day. The mice were sacrificed when the tumor volume reached 1000 mm3. Prior to their tumors reaching this size, mice were euthanatized ifthey experienced an evidence of suffering, including inactivity, labored breathing, interfere with posture, locomotion or feeding, weight loss of more than 10 , or ulceration of the tumor. Mice were euthanatized by carbon dioxide.Figure 4. EGF-SubA enhances anti-tumor activity of temozolomide and ionizing radiation. A clonogenic assay was performed to evaluate the potential of EGF-SubA to enhance temozolomide (A) (statistically significant p,0.0001) and radiation-induced (B) cytotoxicity (statistically significant p,0.0024). U251 cells were seeded in six well culture plates and exposed to 1 pM of EGF-SubA 16 h prior to the addition of temozolomide or radiation exposure. Fresh media was then replaced in the culture plates after 8 h, and surviving fractions were calculated 10 to 14 d following treatment, normalizing for the individual cytotoxicity of EGF-SubA. Each figure is a representative of three independent experiments. doi:10.1371/journal.pone.0052265.gTargeting the UPR in Glioblastoma with EGF-SubAFigure 5. Acidic pH activates the UPR pathway and enhances EGF-SubA cytotoxicity. U251 cells grown in RPMI media whose pH was adjusted to 6.7 and 7.0 with 1N HCl for 3 passages prior to performing experiments demonstrated UPR activation, as determined by PERK phosphorylation (A; pPERK), Xbp1 splicing and increased GRP78 transcription (B). (C) To determine if cells grown in acidic conditions influenced EGFSubA cytotoxicity, a clonogenic assay was performed with U251 cells grown in normal (pH 7.4) or acidic (pH 6.7) conditions at the stated concentrations. Cell survival was significantly different between cells grown in normal and acidic pH at higher doses of EGF SubA (p,0.0001 at 2.5 18325633 pM). Each figure is a representative of three independent experiments. doi:10.1371/journal.pone.0052265.gxCELLigenceCell proliferation under normal and treated condit.
]]>http://www.pi4kinhibitor.com/2017/09/25/study-u251-cells-56106-were-injected-into-the-right-hind-flank-subcutaneously/feed/0Concurrently with the origin of eyespots [6]. Subsequently, many of these genehttp://www.pi4kinhibitor.com/2017/09/25/concurrently-with-the-origin-of-eyespots-6-subsequently-many-of-these-gene/
http://www.pi4kinhibitor.com/2017/09/25/concurrently-with-the-origin-of-eyespots-6-subsequently-many-of-these-gene/#commentsMon, 25 Sep 2017 06:34:21 +0000http://www.pi4kinhibitor.com/?p=4175Concurrently with the origin of eyespots [6]. Subsequently, many of these gene expression patterns were lost from eyespots in a lineage-specific fashion without loss of eyespots. We proposed that this pattern of rapid, perhaps simultaneous, gene expression gains in association with eyespots, could indicate a gene network co-option event that was followedby the elimination of genes that did not play a role in the development of the novel trait [6]. The same could apply to members of the Hh signaling pathway. All members being coopted at the same time, as part of a larger network, and some members, such as hh and ptc, being lost in the lineage leading to B. anynana. This gene loss would imply that Hh signaling was not critical for eyespot development in the early nymphalid ancestors. The retention of the whole pathway in J. coenia could result from the pathway having been secondarily co-opted to function in eyespot development later in this lineage. An alternative scenario to the single origin of multiple eyespot-associated genes via gene network co-option is a more gradual process of eyespot network modification via lineage-specific additions. Under this scenario, hh and ptc are co-opted to the J. coenia lineage allowing Hh signaling to become functional in this lineage but not in B. anynana. Comparative work showed that late additions to the cluster of genes associated with eyespot origins are possible as the gene Antennapedia was co-opted into the eyespot centers late and independently in two nymphalid lineages [6,7]. Only future comparative work involving GR79236 several more species, however, will determine how exactly hh and ptc expression in butterfly eyespots evolved. In conclusion, this work documents an example of a conserved wing pattern, the eyespot, with a single origin within nymphalid butterflies [6] that displays a different developmental basis in different lineages. In one lineage Hh signaling influences adult eyespot size, whereas in another lineage it does not. This example adds to others in the evo-devo literature [2?,38], where different genes and developmental mechanisms pattern homologous traits.AcknowledgmentsWe thank Fred Nijhout and Laura Grunert for J. coenia eggs, Diane Ramos for engrailed primer sequences, Jeffrey Oliver, Diane Ramos, and two anonymous reviewers for comments on the manuscript, and Chris Bollick, Robert Rak, and Eric Larson for growing the corn plants to feed B. anynana larvae.Author ContributionsConceived and designed the experiments: XT AL AM. Performed the experiments: XT AL. Analyzed the data: XT AL AM. Wrote the paper: XT AL AM.Liver cirrhosis is characterized by disturbances in the systemic circulation, including marked arterial vasodilation that occurs principally in the splanchnic circulation, reduces the total peripheral vascular resistance and arterial pressure, and GSK0660 web causes a secondary increase in the cardiac output. These abnormalities are central to the development of several major complications in patients 1379592 with cirrhosis, such as the hepatorenal syndrome, ascites, spontaneous bacterial peritonitis, dilutional hyponatremia, and hepatopulmonary syndrome. Renal failure is the most clinically relevant condition among these conditions because its appearance generally indicates a very poor prognosis [1?0].We developed the MBRS scoring system, a simple prognostic model that includes determination of mean arterial pressure (MAP) and serum bilirubin level and assessment of acute respiratory failure.Concurrently with the origin of eyespots [6]. Subsequently, many of these gene expression patterns were lost from eyespots in a lineage-specific fashion without loss of eyespots. We proposed that this pattern of rapid, perhaps simultaneous, gene expression gains in association with eyespots, could indicate a gene network co-option event that was followedby the elimination of genes that did not play a role in the development of the novel trait [6]. The same could apply to members of the Hh signaling pathway. All members being coopted at the same time, as part of a larger network, and some members, such as hh and ptc, being lost in the lineage leading to B. anynana. This gene loss would imply that Hh signaling was not critical for eyespot development in the early nymphalid ancestors. The retention of the whole pathway in J. coenia could result from the pathway having been secondarily co-opted to function in eyespot development later in this lineage. An alternative scenario to the single origin of multiple eyespot-associated genes via gene network co-option is a more gradual process of eyespot network modification via lineage-specific additions. Under this scenario, hh and ptc are co-opted to the J. coenia lineage allowing Hh signaling to become functional in this lineage but not in B. anynana. Comparative work showed that late additions to the cluster of genes associated with eyespot origins are possible as the gene Antennapedia was co-opted into the eyespot centers late and independently in two nymphalid lineages [6,7]. Only future comparative work involving several more species, however, will determine how exactly hh and ptc expression in butterfly eyespots evolved. In conclusion, this work documents an example of a conserved wing pattern, the eyespot, with a single origin within nymphalid butterflies [6] that displays a different developmental basis in different lineages. In one lineage Hh signaling influences adult eyespot size, whereas in another lineage it does not. This example adds to others in the evo-devo literature [2?,38], where different genes and developmental mechanisms pattern homologous traits.AcknowledgmentsWe thank Fred Nijhout and Laura Grunert for J. coenia eggs, Diane Ramos for engrailed primer sequences, Jeffrey Oliver, Diane Ramos, and two anonymous reviewers for comments on the manuscript, and Chris Bollick, Robert Rak, and Eric Larson for growing the corn plants to feed B. anynana larvae.Author ContributionsConceived and designed the experiments: XT AL AM. Performed the experiments: XT AL. Analyzed the data: XT AL AM. Wrote the paper: XT AL AM.Liver cirrhosis is characterized by disturbances in the systemic circulation, including marked arterial vasodilation that occurs principally in the splanchnic circulation, reduces the total peripheral vascular resistance and arterial pressure, and causes a secondary increase in the cardiac output. These abnormalities are central to the development of several major complications in patients 1379592 with cirrhosis, such as the hepatorenal syndrome, ascites, spontaneous bacterial peritonitis, dilutional hyponatremia, and hepatopulmonary syndrome. Renal failure is the most clinically relevant condition among these conditions because its appearance generally indicates a very poor prognosis [1?0].We developed the MBRS scoring system, a simple prognostic model that includes determination of mean arterial pressure (MAP) and serum bilirubin level and assessment of acute respiratory failure.
]]>http://www.pi4kinhibitor.com/2017/09/25/concurrently-with-the-origin-of-eyespots-6-subsequently-many-of-these-gene/feed/0